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Deafness, Congenital, with Inner Ear Agenesis, Microtia, and Microdontia via the FGF3 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
FGF3 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
4155FGF381479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information. If the Sanger option is selected, CNV detection may be ordered through Test #600.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Ben Dorshorst, PhD

Clinical Features and Genetics

Clinical Features

Congenital deafness with inner ear agenesis, microtia, and microdontia, also known as deafness with labyrinthine aplasia, microtia, and microdontia (LAMM) or Michel aplasia, microdontia, and malformation of the inner ear, is characterized by profound congenital sensorineural hearing loss combined with slightly smaller ears (type I microtia) and smaller teeth (microdontia) that are often widely spaced apart (Alsmadi et al. 2009). The ears of LAMM patients generally show shortened auricles, particularly at the crura of the antihelix. Computed tomography imaging of the temporal bones of LAMM patients often show complete bilateral absence of structures of the inner ear, which include the cochlea, vestibule, and semicircular canals. However, the middle ear of LAMM patients remains intact. Although physical examination of individuals with LAMM generates normal results, they are generally delayed in motor development during infancy, mainly due to impaired balance that is caused by the absence of structures of the inner ear. Despite their hearing impairment, LAMM patients have normal cognitive abilities and do not experience difficulties in writing or reading. Certain patients with LAMM may present less prominent dental as well as external ear features, yet their inner ear often present structural abnormalities (Riazuddin et al. 2011). The symptoms of small ears and teeth are also observed in patients with lacrimoauriculodentodigital (LADD) syndrome (Mathrawala and Hegde 2011).


Congenital deafness with inner ear agenesis, microtia, and microdontia is an autosomal recessive hearing disorder that is caused by pathogenic sequence variants in the fibroblast growth factor 3 (FGF3) gene, which is located in chromosome 11q13.3 (Casey et al. 1986). The FGF3 gene consists of 3 coding exons that encode a 239-amino acid oncoprotein, which is mainly expressed in the rhombencephalon during fetal development when inner ear induction occurs, acting as a signal for the formation of the otic vesicle (Frenz et al. 2010). Disease-causing sequence variants in the FGF3 gene have also been implicated in three other disorders, namely, otodental syndrome (characterized by grossly enlarged molar teeth and high-frequency sensorineural hearing loss), craniosynostosis (a birth defect that involves premature fusion of the skull bones of an infant, thereby changing the growth pattern of the skull), and odontoma-dysphagia syndrome (presents with grossly enlarged, clustered teeth, slight facial abnormalities, and difficulty to swallow) (Gregory-Evans et al. 2007; Grillo et al. 2014). To date, a total of about 20 pathogenic FGF3 sequence variants have been reported, which include 10 missense/nonsense and 4 small deletions that cause LAMM, 3 gross deletions that cause otodental syndrome, and 2 gross insertions that cause craniosynostosis, and 1 gross insertion that causes odontoma-dysphagia (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

No large-scale studies have been conducted on sequence variants in the FGF3 gene, thus its clinical sensitivity is unclear. Of the seven available reports on pathogenic sequence variants in the FGF3 gene, two were case reports (Dill et al. 2011; Singh et al. 2014), whereas five were small-scale family studies consisting of 1 to 3 families, with each family having 2 to 21 affected members (Tekin et al. 2007; Alsmadi et al. 2009; Riazuddin et al. 2011; Sensi et al. 2011; Schaefer et al. 2014).

Testing Strategy

This test provides full coverage of all coding exons of the FGF3 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

The ideal FGF3 test candidates are individuals who present with congenital, profound, autosomal recessive nonsyndromic hearing loss with complete absence of the inner ear, microtia, and microdontia. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in FGF3.


Official Gene Symbol OMIM ID
FGF3 164950
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Alsmadi O. et al. 2009. European Journal of Human Genetics : Ejhg. 17: 14-21. PubMed ID: 18701883
  • Casey G. et al. 1986. Molecular and Cellular Biology. 6: 502-10. PubMed ID: 3023852
  • Dill P. et al. 2011. Molecular Genetics and Metabolism. 104: 362-8. PubMed ID: 21752681
  • Frenz DA. et al. 2010. American Journal of Medical Genetics. Part A. 152A: 2947-61. PubMed ID: 21108385
  • Gregory-Evans CY. et al. 2007. Human Molecular Genetics. 16: 2482-93. PubMed ID: 17656375
  • Grillo L. et al. 2014. Gene. 534: 435-9. PubMed ID: 24120895
  • Human Gene Mutation Database (Bio-base).
  • Mathrawala N.R., Hegde R.J. 2011. Journal of the Indian Society of Pedodontics and Preventive Dentistry. 29: 168-70. PubMed ID: 21911959
  • Riazuddin S. et al. 2011. Bmc Medical Genetics. 12: 21. PubMed ID: 21306635
  • Sensi A. et al. 2011. American Journal of Medical Genetics. Part A. 155A: 1096-101. PubMed ID: 21480479
  • Singh A. et al. 2014. Indian Pediatrics. 51: 919-20. PubMed ID: 25432227
  • Tekin M. et al. 2007. American Journal of Human Genetics. 80: 338-44. PubMed ID: 17236138


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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